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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctgttattcggaatcattaatttgcagatgtattatttgtgctagttctaatggttggtggtatgctgtactgatgtctgtgatgtgtttggttgcagCGTTTTGCTGCTGTCATTATGAGGATAAGAGATCCCAAAACAACTGCACTTATTTTTGCTTCTGGCAAGATG

Basic information

species Glycine max
transcript GLYMA16G25450.4
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G25450.3 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 3
-ttctgttat--tcggaatcattaatttgcagatgtattatttgtgctagttctaatggttggtggtatgctgtactgatgtctgtgatgtgtttggttgcagCGTTTTGCTGCTGTCATTATGAGGATAAGAGATCCCAAAACAACTGCACTTATTTTTGCTTCTGGCAAGATG
  || |||||  |   ||| ||  | |  || |||  |  ||| |||||  | |  |   |  |  |||  | |  |  || |  |  | | | ||    |||||||||||||| ||||| ||||| |||||||| |||||||| || ||||| || ||||| || || || |||
tctcagttatgatgataatgatataatgtcacatgc-tggtttttgctaagttttctctctattattatatttttatcttgaccct--tttatctgtaaacagCGTTTTGCTGCAGTCATCATGAGAATAAGAGAACCCAAAACCACAGCACTGATATTTGCATCGGGTAAAATG

upper sequence: GLYMA16G25450.3 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 2
--ttctgttattcggaatcattaatt--tgcagatgtattatttgtgctagttctaatggttggtggtatgctgtactgatgtctgtgatgtgtttggttgcagCGTTTTGCTGCTGTCATTATGAGGATAAGAGATCCCAAAACAACTGCACTTATTTTTGCTTCTGGCAAGATG
  |||| || || |  || ||||  |  || ||     | |||| ||||   | |  |   |  |  |||  |||| || || || |  | | | ||    |||||||||||||| || || ||||| |||||||| |||||||| || ||||| || ||||| || || || |||
cattct-ttctttgttatgattatataatgtagcaacctgatttttgctgtgttttctcagttattatattttgta-tgttgactct--tttatctgtaaacagCGTTTTGCTGCAGTAATCATGAGAATAAGAGAACCCAAAACCACGGCACTGATATTTGCATCGGGTAAAATG

upper sequence: GLYMA16G25450.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 3
-ttctgttattcggaatcattaatttgcagatgtattatttgtgctagttctaatggttggtggtatgctgtactgatgtctgtgatgtgtt-tggttgcagCGTTTTGCTGCTGTCATTATGAGGATAAGAGATCCCAAAACAACTGCACTTATTTTTGCTTCTGGCAAGATG
  ||      |     |  ||    |   |  | | | ||| | ||    ||| | ||||   || |  | ||   || |      | || | |   |||||||||||||||| || || ||||||||||| || || ||||| || ||  | || ||||||||||| ||||||
gatcaacatcttaaccttgtt--cctattggaggaattttttttctttccctatttgttgccagttttttttatgtattttaaatttatgatgttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|13789639|gb|BG652230.1|BG652230
EST:     ACCTCAAAACAATTGCACTTCAAGCTCGTAATGCAGAGTACAATCCCAAG                         CGTTTTGCTGCTGTCATTATGAGGATAAGAGATCCCAAAACAACTGCACTT
genomic: ACCTCAAAACAATTGCACTTCAAGCTCGTAATGCAGAGTACAATCCCAAGgcaagtttca ... ttggttgcagCGTTTTGCTGCTGTCATTATGAGGATAAGAGATCCCAAAACAACTGCACTT
EST: gi|208239540|gb|GE038626.1|GE038626
EST:     ATGCAGAGTACAATCCCAAG                         CGTTTTGCTGCTGTCATTATGAGGATAAGAGATCCCAAAACAACTGCACTT
genomic: ATGCAGAGTACAATCCCAAGgcaagtttca ... ttggttgcagCGTTTTGCTGCTGTCATTATGAGGATAAGAGATCCCAAAACAACTGCACTT
EST: gi|254320724|gb|GR827173.1|GR827173
EST:     ACCTCAAAACAATTGCACTTCAAGCTCGTAATGCAGAGTACAATCCCAAG                         CGTTTTGCTGCTGTCATTATGAGGATAAGAGATCCCAAAACAACTGCACTT
genomic: ACCTCAAAACAATTGCACTTCAAGCTCGTAATGCAGAGTACAATCCCAAGgcaagtttca ... ttggttgcagCGTTTTGCTGCTGTCATTATGAGGATAAGAGATCCCAAAACAACTGCACTT
EST: gi|14258923|gb|BG881840.1|BG881840
EST:     ACCTCAAAACAATTGCACTTCAAGCTCGTAATGCAGAGTACAATCCCAAG                         CGTTTTGCTGCTGTCATTATGAGGATAAGAGATCCCAAAACAACTGCACTT
genomic: ACCTCAAAACAATTGCACTTCAAGCTCGTAATGCAGAGTACAATCCCAAGgcaagtttca ... ttggttgcagCGTTTTGCTGCTGTCATTATGAGGATAAGAGATCCCAAAACAACTGCACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttctaatggttggtggtatgctgtactgatgtctgtgatgtgtttggttgcagCGTTTTGCTGCTGTCATTATGAGGATAAGAGATCCCAAAACAACTGCACTTATTTTTGCTTCTGGCAAGATG
                         tactgat  putative branch site (score: 2)
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctgttattcggaatcattaatttgcagatgtattatttgtgctagttctaatggttggtggtatgctgtactgatgtctgtgatgtgtttggttgcagCGTTTTGCTGCTGTCATTATGAGGATAAGAGATCCCAAAACAACTGCACTTATTTTTGCTTCTGGCAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
ttctgtt
- - - - - - - - - - - - -gcagatg
- - - - - - - - - - - - - - - - - - -tttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - -tggttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgtg